update to julia v0.7 & v1.0 (#90)

documentation: update to Documenter v0.20 docstrings for Edge, Node and other types using Distributed (nprocs, pmap), Dates, SpecialFunctions (for lgamma), Random REQUIRE: dependencies versions supporting julia 0.7/1.0 warn() -> @warn or @error or @debug, DEBUG eliminated DEBUGC left in, snaqDebug removed info() -> @info, STDOUT-> stdout, DevNull -> devnull @test_warn -> @test_logs (:warn, msg as regex) @test_nowarn -> @test_logs declare global variables in tests isdefined ismatch -> occursin findin -> findall, find -> findall findfirst returns nothing, not 0 when nothing found srand -> Random.seed! Array constructor with undef indmax -> argmax tic, toc -> time_ns round with digits by kw float( -> parse(Float64 readuntil: needs keep=true to keep the final ; ending Newick format readstring(io) -> read(io, String)` small bug fix in chooseEdgeGamma ShiftNet: value as vector of Float64 PhyloNetworkLinearModel: msng -> nonmissing, like in ModelFormulas, lambda as Float64 replace(string, pattern => replacement, count=k) cholfact -> cholesky + -> .+ eye -> Matrix and I DataFrames: insert! and delete! -> insertcol! and deletecol!; by; df[:,i] -> df[i] to avoid copying expm -> exp eig -> eigen diagm, range Pkg.dir -> dirname(pathof()) head -> first documentation: separate build, install R, checkout master of PhyloPlots, drop MkDocs latest -> dev or stable
JuliaPhylo · Jan 4, 2019 · daeffdc · daeffdc
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diff --git a/.travis.yml b/.travis.yml
@@ -1,12 +1,16 @@
+## Documentation: http://docs.travis-ci.com/user/languages/julia/
 language: julia
-os: # WARNING: any change here must also be done in docs/make.jl
+sudo: required
+os:
   - linux
   - osx
-julia: # WARNING: any change here must also be done in docs/make.jl
-# - release
-  - 0.6
+julia:
+  - 0.7
+  - 1.0
+
 notifications:
   email: false
+
 ## Following 4 lines are taken from here:
 # https://github.com/JuliaOpt/NLopt.jl/blob/master/.travis.yml#L10
 # They're meant to fix the NLopt build on Linux.
@@ -15,17 +19,23 @@ addons:
         packages:
             - libnlopt0 # We install it this way to be able to run Travis with `sudo: false`
 
-after_success:
-  # push coverage results to Coveralls
-  - julia -e 'cd(Pkg.dir("PhyloNetworks")); Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())'
-  # push coverage results to Codecov
-  - julia -e 'cd(Pkg.dir("PhyloNetworks")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
-  # Install R
-  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9; fi
-  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo add-apt-repository -y "deb http://cran.rstudio.com/bin/linux/ubuntu $(lsb_release -s -c)/"; fi
-  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo apt-get update -qq -y; fi
-  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo apt-get install git r-base r-base-dev r-recommended -y; fi
-  # - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo R -e 'install.packages("ggplot2", dep=TRUE, repos="http://cran.us.r-project.org")'; fi # takes ~ 6min 2018-06-02
-  # build doc
-  - chmod +x docs/make.sh
-  - ./docs/make.sh
+codecov: true
+coveralls: true
+
+jobs:
+  include:
+    - stage: "Documentation"
+      julia: 1.0
+      os: linux
+      script:
+        - julia --project=docs/ -e 'using Pkg; Pkg.instantiate();
+                                    Pkg.develop(PackageSpec(path=pwd()))'
+        - julia --project=docs/ docs/make.jl
+      before_script:
+        # Install R
+        - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9; fi
+        - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo add-apt-repository -y "deb http://cran.rstudio.com/bin/linux/ubuntu $(lsb_release -s -c)/"; fi
+        - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo apt-get update -qq -y; fi
+        - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo apt-get install git r-base r-base-dev r-recommended -y; fi
+      # - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo R -e 'install.packages("ggplot2", dep=TRUE, repos="http://cran.us.r-project.org")'; fi # takes ~ 6min 2018-06-02
+      after_success: skip
diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@
 
 [![Build Status](https://travis-ci.org/crsl4/PhyloNetworks.jl.svg)](https://travis-ci.org/crsl4/PhyloNetworks.jl)
 [![](https://img.shields.io/badge/docs-stable-blue.svg)](https://crsl4.github.io/PhyloNetworks.jl/stable)
-[![](https://img.shields.io/badge/docs-latest-blue.svg)](https://crsl4.github.io/PhyloNetworks.jl/latest)
+[![](https://img.shields.io/badge/docs-dev-blue.svg)](https://crsl4.github.io/PhyloNetworks.jl/dev)
 [![codecov.io](http://codecov.io/github/crsl4/PhyloNetworks.jl/coverage.svg?branch=master)](http://codecov.io/github/crsl4/PhyloNetworks.jl?branch=master)
 [![Coverage Status](https://coveralls.io/repos/crsl4/PhyloNetworks.jl/badge.svg?branch=master&service=github)](https://coveralls.io/github/crsl4/PhyloNetworks?branch=master)
 
@@ -27,7 +27,7 @@ PhyloNetworks is a [Julia](http://julialang.org) package with utilities to:
 
 To get help, check
 
-- the [latest documentation](https://crsl4.github.io/PhyloNetworks.jl/latest)
+- the [latest documentation](https://crsl4.github.io/PhyloNetworks.jl/dev)
 - the [wiki](https://github.com/crsl4/PhyloNetworks.jl/wiki) for a step-by-step tutorial
   (July 2018) with background on networks
 - the [google group](https://groups.google.com/forum/#!forum/phylonetworks-users)
@@ -36,7 +36,11 @@ To get help, check
 
 If you use the package, please cite
 
-- Claudia Sol&iacute;s-Lemus, Paul Bastide and C&eacute;cile An&eacute; (2017). PhyloNetworks: a package for phylogenetic networks. [Molecular Biology and Evolution](https://academic.oup.com/mbe/article/doi/10.1093/molbev/msx235/4103410/PhyloNetworks-a-package-for-phylogenetic-networks?guestAccessKey=230afceb-df28-4160-832d-aa7c73f86369) doi: 10.1093/molbev/msx235
+- Claudia Sol&iacute;s-Lemus, Paul Bastide and C&eacute;cile An&eacute; (2017).
+  PhyloNetworks: a package for phylogenetic networks.
+  [Molecular Biology and Evolution](https://academic.oup.com/mbe/article/doi/10.1093/molbev/msx235/4103410/PhyloNetworks-a-package-for-phylogenetic-networks?guestAccessKey=230afceb-df28-4160-832d-aa7c73f86369)
+  34(12):3292–3298.
+  [doi:10.1093/molbev/msx235](https://doi.org/10.1093/molbev/msx235)
 
 ## Maximum pseudolikelihood estimation of species network: SNaQ <img src="http://pages.stat.wisc.edu/~claudia/Images/snaq.png" align=right title="SNaQ logo" width=262.5 height=111>
 <!-- ![SNaQ logo](http://pages.stat.wisc.edu/~claudia/Images/snaq.png)
@@ -54,7 +58,8 @@ If you use SNaQ, please cite
 - Claudia Sol&iacute;s-Lemus and C&eacute;cile An&eacute; (2016).
   Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting.
   [PLoS Genet](http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005896)
-  12(3):e1005896. doi: 10.1371/journal.pgen.1005896
+  12(3):e1005896.
+  [doi:10.1371/journal.pgen.1005896](https://doi.org/10.1371/journal.pgen.1005896)
 
 ## Phylogenetic comparative methods for trait evolution
 
@@ -63,7 +68,7 @@ with or without transgressive evolution after reticulations:
 
 - Bastide, Solís-Lemus, Kriebel, Sparks, Ané (2018).
   Phylogenetic Comparative Methods for Phylogenetic Networks with Reticulations.
-  Systematic Biology.
+  Systematic Biology, 67(5):800–820.
   [doi:10.1093/sysbio/syy033](https://doi.org/10.1093/sysbio/syy033).
   SI on [dryad](http://dx.doi.org/10.5061/dryad.nt2g6)
   including a [tutorial for trait evolution](https://datadryad.org/bitstream/handle/10255/dryad.177752/xiphophorus_PCM_analysis.html?sequence=1)

diff --git a/REQUIRE b/REQUIRE
@@ -1,12 +1,14 @@
-julia 0.6 0.7-
-BioSequences 0.7
-BioSymbols 1.0
-Combinatorics 0.2.1
-CSV 0.2.1
-DataFrames 0.11 # requires and re-exports Missings
-DataStructures 0.5.2
-GLM 0.10 # requires StatsModels, Distributions
-NLopt 0.3
-StaticArrays 0.6.0
-StatsBase 0.22
-StatsFuns 0.6.1
+julia 0.7
+BioSequences 1.0
+BioSymbols 3.0
+Combinatorics 0.7
+CSV 0.4
+DataFrames 0.13
+DataStructures 0.9
+GLM 1.0
+NLopt 0.5.1
+SpecialFunctions 0.7
+StaticArrays 0.8.3
+StatsBase 0.26
+StatsFuns 0.7
+StatsModels 0.3
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -0,0 +1,16 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterMarkdown = "997ab1e6-3595-5248-9280-8efb232c3433"
+# will be added by Travis as being developed:
+# PhyloNetworks = "33ad39ac-ed31-50eb-9b15-43d0656eaa72"
+# packages used in the manual pages:
+CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+# will be added to track master version in make.jl:
+# PhyloPlots = "c0d5b6db-e3fc-52bc-a87d-1d050989ed3b"
+RCall = "6f49c342-dc21-5d91-9882-a32aef131414"
+StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
+StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
+
+[compat]
+Documenter = "~0.21"
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,13 +1,37 @@
-using Documenter, PhyloNetworks
+using Documenter, DocumenterMarkdown
 
-makedocs()
+using Pkg
+Pkg.add(PackageSpec(name="PhyloPlots", rev="master"))
+
+using PhyloNetworks
+
+makedocs(
+    sitename = "PhyloNetworks.jl",
+    authors = "Claudia Solís-Lemus, Cécile Ané, Paul Bastide and contributors.",
+    modules = [PhyloNetworks], # to list methods from PhyloNetworks only, not from Base etc.
+    format = Documenter.HTML(prettyurls = get(ENV, "CI", nothing) == "true"), # easier local build
+    pages = [
+        "Home" => "index.md",
+        "Manual" => [
+            "Installation" => "man/installation.md",
+            "Input Data for SNaQ" => "man/inputdata.md",
+            "TICR pipeline" => "man/ticr_howtogetQuartetCFs.md",
+            "Network estimation and display" => "man/snaq_plot.md",
+            "Network comparison and manipulation" => "man/dist_reroot.md",
+            "Candidate Networks" => "man/fixednetworkoptim.md",
+            "Extract Expected CFs" => "man/expectedCFs.md",
+            "Bootstrap" => "man/bootstrap.md",
+            "Multiple Alleles" => "man/multiplealleles.md",
+            "Continuous Trait Evolution" => "man/trait_tree.md",
+            "Parsimony on networks" => "man/parsimony.md",
+        ],
+        "Library" => [
+            "Public" => "lib/public.md",
+            "Internals" => "lib/internals.md",
+        ]
+    ],
+)
 
-# Versions of `mkdocs` and `mkdocs-material` specified manually to avoid conflicts. 
-# See here: https://discourse.julialang.org/t/mkdocs-material-in-documenter/13764/3
-# To be kept in mind: those versions might evolve in the future.
 deploydocs(
-    deps   = Deps.pip("pygments", "mkdocs==0.17.5", "mkdocs-material==2.9.4", "python-markdown-math"),
-    repo = "github.com/crsl4/PhyloNetworks.jl.git",
-    julia  = "0.6",
-    osname = "linux"
+    repo = "github.com/crsl4/PhyloNetworks.jl.git"
 )
diff --git a/docs/make.sh b/docs/make.sh
diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml